Transcriptomic similarities and differences in host response between SARS-CoV-2 and other viral infections

Thair, Simone A.; He, Yudong D.; Hasin-Brumshtein, Yehudit; Sakaram, Suraj; Pandya, Rushika; Toh, Jiaying; Rawling, David; Remmel, Melissa; Coyle, Sabrina; Dalekos, George N.; Koutsodimitropoulos, Ioannis; Vlachogianni, Glykeria; Gkeka, Eleni; Karakike, Eleni; Damoraki, Georgia; Antonakos, Nikolaos; Khatri, Purvesh; Giamarellos-Bourboulis, Evangelos J.; Sweeney, Timothy E.

The pandemic 2019 novel coronavirus disease (COVID-19) shares certain clinical characteristics with other acute viral infections. We studied the whole-blood transcriptomic host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using RNAseq from 24 healthy controls and 62 prospectively enrolled patients with COVID-19. We then compared these data to non-COVID-19 viral infections, curated from 23 independent studies profiling 1,855 blood samples covering six viruses (influenza, respiratory syncytial virus (RSV), human rhinovirus (HRV), severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), Ebola, dengue). We show gene expression changes in COVID-19 versus non-COVID-19 viral infections are highly correlated (r = 0.74, p < 0.001). However, we also found 416 genes specific to COVID-19. Inspection of top genes revealed dynamic immune evasion and counter host responses specific to COVID-19. Statistical deconvolution of cell proportions maps many cell type proportions concordantly shifting. Discordantly increased in COVID-19 were CD56(bright) natural killer cells and M2 macrophages. The concordant and discordant responses mapped out here provide a window to explore the pathophysiology of the host response to SARS-CoV-2.